Utility of PCR Amplification and DNA Microarray Hybridization in 16S rDNA for Rapid Diagnosis of Bacteremia Associated with Hematological Malignancies.

The rapid diagnosis of bacteremia is important for patient management and the choice of antimicrobial and antifungal therapy, especially in hematological malignancies. We describe a rapid detection and identification system that uses universal PCR primers and DNA microarray hybridization compared to the conventional culture method. This new DNA-microarray method could be performed within only 24 hours. Eighty-four microorganism probes are spotted onto a microarray plate containing most causal clinical pathogens (Patent No.WO2003/106676). We can detect 93% of pathogen of blood culture by the frequency of upper 28 microorganisms.

We used universal PCR primers to amplify a variable region of bacterial 16S ribosomal DNA or fungal ITS (internal transcribed spacer region) of ribosomal DNA, followed by the reverse hybridization of products to a panel of oligonucleotides. Genomic DNA was extracted from blood with a DNA isolation kit (DNeasy; QIAGEN, CA, USA) according to the manufacturer's instructions. The 16S ribosomal ribonucleic acid gene (16S rDNA) was amplified from genomic DNA using broad-spectrum PCR primers; 5'-AGAGTTTGATCCTGGCT-CAG-3', corresponding to Escherichia coli 16S rDNA positions 8 through 27, and 5'-GTATTACCGCGGCTGCTGG-3', corresponding to Escherichia coli 16S rRNA gene positions 517 through 535. On the other hand, the PCR primers; 5'-TCCGTAGGTGAACCTGCGG-3' and 5'-GCTGCGTTCTTCATCGATGC-3' are used to amplify the ITS 1 region. Thirty-five cycles of amplification were performed in a thermal cycler (Gene Amp PCR system 9600, Perkin-Elmer Cetus, CT, USA). The PCR products from samples were labeled by Cy5- primers and applied to the microarray. The microarray was scanned using a ScanArray 4000 (Axon Instruments, CA, USA) to determine the amount of Cy5-labeled PCR products. Fluorescence intensities were calculated with DNASIS Array software (HITACHI Soft Engineering, Japan). This new identification system using DNA microarray hybridization and the conventional blood culture method (BacT/ALERT, bioMerieux and Bactec, Becton-Dickinson, USA) were applied for 336 infectious episodes from 100 patients with hematological malignancy except 2 patients with aplastic anemia retrospectively from May 2004 to February 2007. The hematological malignancies included 152 episodes of acute myeloid leukemia (45.2%), 106 of non-Hodgkin lymphoma (31.5%), 38 of acute lymphoid leukemia (11.3%), 17 of multiple myeloma (5%), 12 of myelodysplastic syndrome (3.6%), 4 of aplastic anemia (1.2%) etc.

Thirty-nine episodes (11.6%) were positive after a few days of culturing, and 41 episodes (12.2%) were identified by the new microarray method within 24 hours. Both methods yielded positive results 10.7% (36 episodes). Pathogens in most cases were identical at the species level (21/36 episodes 58.3%), some cases were identical at the genus level (6/36 16.7%), in the other cases, several bacteria were detected by each method. A positive DNA microarray and negative blood culture occurred at a rate of 1.5% (5 episodes), with pathogens in these cases being Bacillus cereus, Staphylococcus epidermidis, Chryseobacterium indologenes, and Enterococcus faecium. A negative DNA microarray and positive blood culture occurred at a rate of 0.9% (3 episodes), and with pathogens comprising Staphylococcus aureus, á-Streptococcus, and Pseudomonas aeruginosa. Both methods yielded negative results at a rate of 86.9% (292 episodes). The sensitivity and specificity of this new microarray method were 92.3 and 98.3%, respectively, compared with the conventional blood culture method. Regarding fungal infection, only one episode out of one patient was found to be positive microarray and negative blood culture of Yeast like organism.

This new DNA microarray method has the potential to diagnose bacteremia quickly and detect pathogens at least at the same rate as the conventional blood culture method. Regarding the possibility of improving the sensitivity and specificity, or application for fungal infection further study should be needed. In conclusion, DNA microarray is a useful method for the management of febrile patients with hematological malignancy.

Iwasaki:The ministry of Health, Labour and Welfare of Japan: Research Funding.